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Human Genome News Archive Edition

Human Genome News, Mar.-Apr. 1995; 6(6)

Positional Cloning Approach Expedites Gene Hunts

For most scientists, searching for a disease gene means years of laboring over the mapping, cloning, and sequencing processes and considerably less time actually studying the gene and its function.

But this should soon change. A new approach called "positional candidate" is rapidly coming of age and should streamline the process of identifying disease genes within the next few years.

Based on the growing body of genome resources, the positional candidate strategy lets researchers combine information about a gene's chromosomal location with increasingly detailed genetic and physical maps, allowing for easier identification of a potential causative gene.

According to the latest data, positional candidate studies already have led to the identification of over 50 disease genes. Commenting recently in Nature Genetics, NIH National Center for Human Genome Research Director Francis Collins stated that this more efficient approach is a major reason that positional cloning is moving from the "perditional to traditional" way of finding disease genes.

Strategy Saves Time

One of the most intriguing uses of the positional candidate strategy is the recent identification of the gene causing achondroplasia (ACH), a common form of dwarfism.

The ACH gene story began in 1991 during the marathon race for the gene responsible for Huntington's disease. That year, a group at the University of California, Irvine, reported that it had isolated an interesting cDNA that mapped to the middle of the chromosome 4 subregion possibly containing the Huntington's gene.

This was exciting news. The group, led by John Wasmuth, and other members of the Huntington's Disease Collaborative Research Group had spent nearly 8 years stalking the Huntington's gene in an initiative that Science once described as "a nightmare of false leads, confounding data, and backbreaking work."

The backbreaking work went on. Later studies failed to show that the gene, called FGFR3, played any role in Huntington's. Having already deposited the nucleotide sequence for FGFR3 in GenBank (tm), Wasmuth's group continued to search along the tip of chromosome 4.

The Irvine scientists did not realize it at the time, but this work with the FGFR3 gene would give them a head start later in the hunt for the gene involved in ACH.

Last year, three laboratories reported that linkage studies had localized the ACH gene to a 2.5-Mb stretch on the tip of chromosome 4, the region where the FGFR3 gene resides. This time, investigators had no need to construct clones of the DNA region or design complex disequilibrium studies. With the sequenced FGFR3 gene as their candidate, they acquired patient DNA samples and developed PCR primers to test for possible mutations.

Within a matter of weeks, the Irvine scientists got their answer: 15 of 16 people with ACH had the same point mutation in the FGFR3 gene.

Positional Candidate Strategy Becoming Widely Used

The positional candidate approach relies on a three-step process that saves time and effort: (1) localizing a disease gene to a chromosomal subregion, generally by using traditional linkage analysis; (2) searching databases for an attractive candidate gene within that subregion; and (3) testing the candidate gene for disease-causing mutations.

Not so long ago, accessing a database of mapped genes seemed as futuristic as boarding the Starship Enterprise. With the tremendous progress in mapping human and mouse genomes and improving gene-discovery techniques, the positional candidate strategy already has amassed an impressive list of gene discoveries.

Since 1990, scientists have used this approach to find genes implicated in such conditions as Marfan syndrome, inherited nonpolyposis colon cancer, retinitis pigmentosa, long QT syndrome, Jackson-Weiss syndrome, Crouzon syndrome, Alzheimer's disease, and several others. As impressive as this list is, recent international mapping initiatives promise to put many more human genes on the map during the next few years and make positional candidate investigations even more successful. [see IMAGE Characterizes cDNA Clones]

In February of this year, Washington University and the pharmaceutical company Merck, Sharpe, and Dohme announced the first publicly available installment of 15,000 ESTs. Launched last summer, this ambitious effort is expected to process about 200,000 cDNAs over the next 18 months. Lawrence Livermore National Laboratory is arraying clones from a cDNA library generated at Columbia University.

Meanwhile, an international EST consortium is being coordinated at the Sanger Centre. It includes the Stanford University Genome Center, Wellcome Trust Centre for Human Genetics, Genethon, Washington University, University of Cambridge, and Whitehead Institute Massachusetts Institute of Technology. These groups joined forces to begin mapping 70,000 ESTs to 0.5-Mb intervals or better. To help speed this important initiative along, The Institute of Genomic Research donated primers for 15,000 ESTs.

Looking to the Future

Still, several challenges remain before positional candidate strategies become firmly entrenched. One concern is the need for a more comprehensive database of mapped genes. Although well over 4000 genes have been mapped, tens of thousands more must be identified to fill in blanks in the human genome.

At the same time, standard positional cloning efforts usually result in candidate intervals of 0.5 to 5 Mb, but mapping cDNAs to traditional somatic cell hybrids or by using FISH usually will not achieve this degree of resolution. Large-insert clone libraries or radiation hybrids may be needed to provide the necessary resolution.

Despite these challenges, both of which are now being addressed successfully, most experts are encouraged by the short-term success of positional candidate studies. "With all the cDNA activity alone, it seems likely that more than half the human transcripts will be placed on the human genome map in the next 18 months," predicted Collins. "The effect on the success rate of the positional candidate approach should be profound."
Bob Kuska, NCHGR


"Postitional Cloning Moves from Perditional to Traditional," by Francis Collins, appeared in Nature Genetics [9(4), 347-50 (April 1995)].


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Human Genome Project 1990–2003

The Human Genome Project (HGP) was an international 13-year effort, 1990 to 2003. Primary goals were to discover the complete set of human genes and make them accessible for further biological study, and determine the complete sequence of DNA bases in the human genome. See Timeline for more HGP history.

Human Genome News

Published from 1989 until 2002, this newsletter facilitated HGP communication, helped prevent duplication of research effort, and informed persons interested in genome research.